词条 | Synthetic genetic array |
释义 |
BackgroundSynthetic genetic array analysis was initially developed by Tong et al.[1] in 2001 and has since been used by many groups working in a wide range of biomedical fields. SGA utilizes the entire genome yeast knock-out set created by the yeast genome deletion project.[8] ProcedureSynthetic genetic array analysis is generally conducted using colony arrays on petriplates at standard densities (96, 384, 768, 1536). To perform a SGA analysis in S.cerevisae, the query gene deletion is crossed systematically with a deletion mutant array (DMA) containing every viable knockout ORF of the yeast genome (currently 4786 strains).[9] The resulting diploids are then sporulated by transferring to a media containing reduced nitrogen. The haploid progeny are then put through a series of selection platings and incubations to select for double mutants. The double mutants are screened for SSL interactions visually or using imaging software by assessing the size of the resulting colonies. RoboticsDue to the large number of precise replication steps in SGA analysis, robots are widely used to perform the colony manipulations. There are a few systems specifically designed for SGA analysis, which greatly decrease the time to analyse a query gene. Generally these have a series of pins which are used to transfer cells to and from plates, with one system utilizing disposable pads of pins to eliminate washing cycles. Computer programs can be used to analyze the colony sizes from images of the plates thus automating the SGA scoring and chemical-genetics profiling. Step for a yeast high content genome-wide genetic screening system(SGA -road map)There are six major components
The first step is to collect the mutants and create a mutants library either in solid or liquid media. Solid media could be better because it could save lots of time. At Early stage, mutant creation was done by homologous recombination method. We have an excellent mutant library for Saccharomyces cerevisiae, a well-studied model organism. However, if you are trying for new, yeast model, you could have to either a genome sequencing and can predict the possible ORF by the good reference yeast genome(For example: with Saccharomyces cerevisiae). Consider a special case: If you don’t have a reference genome, you should go for transcriptome and genome analysis of that new model organism.
Mutant collectionSee also
References1. ^1 {{Cite journal | last1 = Tong | first1 = A. H. Y. | last2 = Evangelista | first2 = M. | last3 = Parsons | first3 = A. B. | last4 = Xu | first4 = H. | last5 = Bader | first5 = G. D. | last6 = Pagé | first6 = N. | last7 = Robinson | first7 = M. | last8 = Raghibizadeh | first8 = S. | last9 = Hogue | first9 = C. W. | last10 = Bussey | first10 = H. | last11 = Andrews | first11 = B. | last12 = Tyers | first12 = M. | last13 = Boone | first13 = C. | title = Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants | doi = 10.1126/science.1065810 | journal = Science | volume = 294 | issue = 5550 | pages = 2364–2368 | year = 2001 | pmid = 11743205 | pmc = }} 2. ^{{Cite journal | last1 = Tong | first1 = A. H. Y. | last2 = Lesage | first2 = G. | last3 = Bader | first3 = G. D. | last4 = Ding | first4 = H. | last5 = Xu | first5 = H. | last6 = Xin | first6 = X. | last7 = Young | first7 = J. | last8 = Berriz | first8 = G. F. | last9 = Brost | first9 = R. L. | last10 = Chang | first10 = M. | last11 = Chen | first11 = Y. | last12 = Cheng | first12 = X. | last13 = Chua | first13 = G. | last14 = Friesen | first14 = H. | last15 = Goldberg | first15 = D. S. | last16 = Haynes | first16 = J. | last17 = Humphries | first17 = C. | last18 = He | first18 = G. | last19 = Hussein | first19 = S. | last20 = Ke | first20 = L. | last21 = Krogan | first21 = N. | last22 = Li | first22 = Z. | last23 = Levinson | first23 = J. N. | last24 = Lu | first24 = H. | last25 = Ménard | first25 = P. | last26 = Munyana | first26 = C. | last27 = Parsons | first27 = A. B. | last28 = Ryan | first28 = O. | last29 = Tonikian | first29 = R. | last30 = Roberts | first30 = T. | title = Global Mapping of the Yeast Genetic Interaction Network | doi = 10.1126/science.1091317 | journal = Science | volume = 303 | issue = 5659 | pages = 808–813 | year = 2004 | pmid = 14764870 | pmc = }} 3. ^{{Cite journal | last1 = Costanzo | first1 = M. | last2 = Baryshnikova | first2 = A. | last3 = Bellay | first3 = J. | last4 = Kim | first4 = Y. | last5 = Spear | first5 = E. D. | last6 = Sevier | first6 = C. S. | last7 = Ding | first7 = H. | last8 = Koh | first8 = J. L. Y. | last9 = Toufighi | first9 = K. | last10 = Mostafavi | doi = 10.1126/science.1180823 | first10 = S. | last11 = Prinz | first11 = J. | last12 = St Onge | first12 = R. P. | last13 = Vandersluis | first13 = B. | last14 = Makhnevych | first14 = T. | last15 = Vizeacoumar | first15 = F. J. | last16 = Alizadeh | first16 = S. | last17 = Bahr | first17 = S. | last18 = Brost | first18 = R. L. | last19 = Chen | first19 = Y. | last20 = Cokol | first20 = M. | last21 = Deshpande | first21 = R. | last22 = Li | first22 = Z. | last23 = Lin | first23 = Z. -Y. | last24 = Liang | first24 = W. | last25 = Marback | first25 = M. | last26 = Paw | first26 = J. | last27 = San Luis | first27 = B. -J. | last28 = Shuteriqi | first28 = E. | last29 = Tong | first29 = A. H. Y. | last30 = Van Dyk | first30 = N. | title = The Genetic Landscape of a Cell | journal = Science | volume = 327 | issue = 5964 | pages = 425–431 | year = 2010 | pmid = 20093466 | pmc = 5600254}} 4. ^{{Cite journal | last1 = Roguev | first1 = A. | last2 = Wiren | first2 = M. | last3 = Weissman | first3 = J. S. | last4 = Krogan | first4 = N. J. | title = High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe | doi = 10.1038/nmeth1098 | journal = Nature Methods | volume = 4 | issue = 10 | pages = 861–866 | year = 2007 | pmid = 17893680 | pmc = }} 5. ^{{Cite journal | last1 = Dixon | first1 = S. J. | last2 = Fedyshyn | first2 = Y. | last3 = Koh | first3 = J. L. Y. | last4 = Prasad | first4 = T. S. K. | last5 = Chahwan | first5 = C. | last6 = Chua | first6 = G. | last7 = Toufighi | first7 = K. | last8 = Baryshnikova | first8 = A. | last9 = Hayles | first9 = J. | last10 = Hoe | doi = 10.1073/pnas.0806261105 | first10 = K. -L. | last11 = Kim | first11 = D. -U. | last12 = Park | first12 = H. -O. | last13 = Myers | first13 = C. L. | last14 = Pandey | first14 = A. | last15 = Durocher | first15 = D. | last16 = Andrews | first16 = B. J. | last17 = Boone | first17 = C. | title = Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes | journal = Proceedings of the National Academy of Sciences | volume = 105 | issue = 43 | pages = 16653–16658 | year = 2008 | pmid = 18931302 | pmc =2575475 }} 6. ^{{Cite journal | doi = 10.1038/nmeth.1240 | last1 = Typas | first1 = A. | last2 = Nichols | first2 = R. J. | last3 = Siegele | first3 = D. A. | last4 = Shales | first4 = M. | last5 = Collins | first5 = S. R. | last6 = Lim | first6 = B. | last7 = Braberg | first7 = H. | last8 = Yamamoto | first8 = N. | last9 = Takeuchi | first9 = R. | last10 = Wanner | first10 = B. L. | last11 = Mori | first11 = H. | last12 = Weissman | first12 = J. S. | last13 = Krogan | first13 = N. J. | last14 = Gross | first14 = C. A. | title = High-throughput, quantitative analyses of genetic interactions in E. Coli | journal = Nature Methods | volume = 5 | issue = 9 | pages = 781–787 | year = 2008 | pmid = 19160513 | pmc = 2700713}} 7. ^{{Cite journal | last1 = Butland | first1 = G. | last2 = Babu | first2 = M. | last3 = Díaz-Mejía | first3 = J. J. | last4 = Bohdana | first4 = F. | last5 = Phanse | first5 = S. | last6 = Gold | first6 = B. | last7 = Yang | first7 = W. | last8 = Li | first8 = J. | last9 = Gagarinova | first9 = A. G. | last10 = Pogoutse | doi = 10.1038/nmeth.1239 | first10 = O. | last11 = Mori | first11 = H. | last12 = Wanner | first12 = B. L. | last13 = Lo | first13 = H. | last14 = Wasniewski | first14 = J. | last15 = Christopolous | first15 = C. | last16 = Ali | first16 = M. | last17 = Venn | first17 = P. | last18 = Safavi-Naini | first18 = A. | last19 = Sourour | first19 = N. | last20 = Caron | first20 = S. | last21 = Choi | first21 = J. Y. | last22 = Laigle | first22 = L. | last23 = Nazarians-Armavil | first23 = A. | last24 = Deshpande | first24 = A. | last25 = Joe | first25 = S. | last26 = Datsenko | first26 = K. A. | last27 = Yamamoto | first27 = N. | last28 = Andrews | first28 = B. J. | last29 = Boone | first29 = C. | last30 = Ding | first30 = H. | title = ESGA: E. Coli synthetic genetic array analysis | journal = Nature Methods | volume = 5 | issue = 9 | pages = 789–795 | year = 2008 | pmid = 18677321 | pmc = }} 8. ^{{cite web|url=http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html|title=Saccharomyces Genome Deletion Project|work=}} 9. ^{{cite web|title=Yeast Knockout Strains |url=http://www.openbiosystems.com/GeneExpression/Yeast/YKO/|archiveurl=https://web.archive.org/web/20111119012937/http://www.openbiosystems.com/GeneExpression/Yeast/YKO/|archivedate=November 19, 2011 |work=Open Biosystems}} 2 : Genetics|Microarrays |
随便看 |
|
开放百科全书收录14589846条英语、德语、日语等多语种百科知识,基本涵盖了大多数领域的百科知识,是一部内容自由、开放的电子版国际百科全书。